
Tumor=$1
Normal=$2
config_file=$3
skip_line=$4

source ${config_file}

export skip_line=`cat ${maf_path}/${Tumor}_${Normal}_PASS.maf | grep -E "##|#version" | wc -l`
${Rscript} ${dna_preprocess_scripts}/mutect2_Scripts/GATK4_SomaticVariant_Qc_Filter.R \
--Tumor ${Tumor} \
--Normal ${Normal} \
--skip_line ${skip_line} \
--maf_file ${maf_path}/${Tumor}_${Normal}_PASS.maf \
--qc_file ${vcf_qc_path}/${Tumor}_${Normal}_MutQc.annotationRegion.csv \
--stand_list_file ${dna_preprocess_scripts}/mutect2_Scripts/QC_Standard.list \
--out_record_file ${vcf_qc_path}/${Tumor}_${Normal}_MutQc.RecordQcNum.csv \
--out_file ${vcf_qc_path}/${Tumor}_${Normal}_MutQc.KeepMut.csv